pept-X: Peptide ⇄ SMILES Converter

Convert between peptide sequences and SMILES strings, extend the monomer library, and sketch new residues directly in the browser.

Sequence → SMILES

Append |S-S: i-j ... to encode disulfide bridges between residue positions (caps excluded). Multiple pairs can be separated by spaces.

Linear peptides only. For cyclic or stapled peptides, use the dedicated cards below. 仅支持线性肽，环肽或装订肽请在下方对应窗口输入。 


        


        

          
SMILES → Sequence

          

            The converter auto-detects disulfide bridges and reports them via
            |S-S: …, so no connectivity information is lost.
          

          

            Linear peptides only. For cyclic or stapled peptides, use the dedicated cards
            below. 仅支持线性肽，环肽或装订肽请在下方对应窗口输入。
          

          

            
            
            
          

          

        

      


      

        

          

            
Template Library & Custom Entries

            

              Browse the combined HELM core library and custom templates, or register new building blocks. A PDF catalog of
              all templates is regenerated from these files—use the button below to download the latest copy.
            

            

              Templates: --
            

          

          

            Download Template Catalog (PDF)
          

        

        

          

            
Add Custom Template

            

              Paste a SMILES string from your preferred drawing tool (for example, Ketcher or ChemDraw) and register it here.
              Newly submitted templates become available immediately and will be included the next time you regenerate the PDF catalog.
            

            

              
              

              
              

              
              

              

                

                  Example 1 · Dimethyl Lysine
                  
Code: LyS_Dimethyl
SMILES: CN(C)CCCC[C@H](N)C(=O)O
Aliases: KX
Components: LyS, Me2

                


                

                  Example 2 · PEGylated Lysine
                  
Code: LyS_1PEG2
SMILES: NCCCC[C@H](NC(=O)OCCOCCO)C(=O)O
Aliases: LysPEG
Components: LyS, PEG2

                


                

                  Example 3 · D-type Norleucine
                  
Code: dNle
SMILES: N[C@@H](CCCC)C(=O)O
Aliases: dNorleucine
Components: dNle

                

              


              
              

              
            

            

          


          

            
Search Template

            
Search the combined core + custom template library by code/alias or SMILES.

            

              
              

              
              

              
            

            

          

        

      


      

        

          
Stapled Sequence → SMILES (v2)

          

            Input format:
            sequence|pose:1 S,6 S,10 S|linker:[*:1]CC1=CC(C[*:6])=CC(C[*:10])=C1.
            Alternatively, use three lines (sequence, pose, linker) separated by newlines.
          

          

            Pose rules: residue indices count peptide residues only (caps excluded).
            Specify the side-chain atom to attach (e.g. S). If the atom is absent, the
            system falls back to the default terminal heavy atom and emits a warning.
            Disulfide bridges can be declared with |S-S: … alongside the pose metadata.
          

          

            
            
              

                Example
                
ac-C-V-T-I-P-C-D-L-W-C-W-I-K-dR-am|pose:1 S,6 S,10 S|linker:[*:1]CC1=CC(C[*:6])=CC(C[*:10])=C1

                
Three-line equivalent:

                
ac-C-V-T-I-P-C-D-L-W-C-W-I-K-dR-am
pose:1 S,6 S,10 S
linker:[*:1]CC1=CC(C[*:6])=CC(C[*:10])=C1

              

            
          

          

        


        

          
SMILES → Stapled Sequence (v2)

          

            Disulfide bridges are also recovered automatically and appear in the sequence metadata.
          

          

            
            
            
          

          

        

      


      

        

          
Cyclic Sequence → SMILES

          

            Provide a head-to-tail peptide sequence without terminal caps. The tool linearises it,
            closes the backbone, and returns a cyclic SMILES. Example:
            C-V-T-I-P-C-D-L-W-C-W-I-K|S-S: 1-6 5-10.
            Once cyclised, the molecule no longer has absolute N/C termini, so any rotation of the
            sequence (starting at a different residue) is chemically equivalent.
          

          

            Disulfide annotations reuse the |S-S: … syntax and refer to positions before
            cyclisation.
          

          

            
            
            
          

          

        


        

          
Cyclic SMILES → Sequence

          

            Paste a cyclic peptide SMILES to recover a sequence (reported in a deterministic rotation)
            plus metadata. The tool breaks one peptide bond, restores termini, and runs the standard
            converter. Because cyclic peptides have no fixed start/end, the reported sequence is just
            one valid rotation; e.g. K-C-…-I can also be written as
            C-…-I-K, V-…-K-C, etc.
          

          

            Existing disulfide bridges are detected automatically and emitted as
            |S-S: … metadata in the returned sequence.
          

          

            
            
            
          

          

        

      


      

        

          
Lariat SMILES → Sequence

          

            Paste a lariat (lasso) peptide SMILES. The converter detects the side-chain iso-peptide bond, linearises the chain,
            and emits a sequence with an optional [C-cap:*…] token plus the |lariat tag.
          

          

            
            
            
          

          

        


        

          
Lariat Sequence → SMILES

          

            Input a lariat sequence ending with |lariat; if present, append [C-cap:*…] to cap the C-terminus
            (the * placeholder bonds to the terminal carbonyl carbon). This builds a linear approximation of the lariat SMILES.
          

          

            
            
            
          

          

        

      


      

        

          
Draw / Edit Structure

          

            Use the embedded JSME editor to sketch a residue or linker. Convert between drawing
            and SMILES, copy the result, or paste an existing SMILES to visualize the structure.
          

          

            

          

          
          
          

            
            
            
            
          

          

        


        

          
Secondary Structure Preview (3D)

          

            Provide any peptide representation below to generate a conformer and visualize the
            coarse secondary structure. The prediction is independent from the conversion cards.
          

          

            

              
SMILES Input

              
Paste a peptide SMILES string.

              
              
              

            


            

              
Linear Sequence

              

                Use the same |S-S: i-j syntax for disulfide bridges as in the converter.
              

              
              
              

            


            

              
Cyclic Sequence

              
Enter a head-to-tail peptide sequence; disulfide syntax is supported.

              
              
              

            


            

              
Stapled Sequence (v2)

              

                Same format as the stapled converter, e.g.
                sequence|pose:…|linker:… or the three-line variant.